BN1762 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 1.2734e-04 8.4206e-04
Layer 3 2.4036e-04 7.3787e-04
Layer 5 3.0930e-04 8.0281e-04
Layer 4 6.3604e-04 1.2455e-03
Layer 6 7.9160e-04 3.9674e-03
WM 9.4553e-01 2.9234e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
ATP5F1B Expression Distribution
Gene Specificity Score (GSS)
ATP5F1B GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
ATP5F1B Layer 5 3.2256 0.8718
ATP5F1A Layer 5 3.3066 0.8705
EEF1A2 Layer 2 3.8877 0.8698
TUBB2A Layer 5 3.8047 0.8690
THY1 Layer 2 3.7070 0.8684
EIF4A2 Layer 5 3.3066 0.8681
ATP1B1 Layer 3 3.5898 0.8679
SYT1 Layer 5 3.6523 0.8671
SNRPN Layer 5 3.3438 0.8667
DKK3 Layer 2 3.2793 0.8667
ATP6V0C Layer 2 3.2422 0.8664
BASP1 Layer 5 3.5977 0.8661
PRNP Layer 5 3.0645 0.8657
NEFL Layer 3 4.0508 0.8654
OLFM1 Layer 4 3.5508 0.8652
UQCRH Layer 4 3.3789 0.8649
RTN3 Layer 5 3.1387 0.8648
GDI1 Layer 4 3.3145 0.8648
ENO2 Layer 4 3.8047 0.8648
SLC22A17 Layer 2 3.3789 0.8646
YWHAH Layer 5 3.4688 0.8642
YWHAB Layer 5 3.3945 0.8638
DNM1 Layer 2 3.5625 0.8635
MDH1 Layer 2 3.7070 0.8633
BEX1 Layer 5 3.6211 0.8629
PRKAR1B Layer 5 3.2607 0.8629
OAZ1 Layer 5 3.1465 0.8627
ATP5MD Layer 2 3.2793 0.8624
MORF4L1 Layer 5 3.4043 0.8622
RTN1 Layer 5 3.6836 0.8620
CHN1 Layer 3 3.4004 0.8606
SARAF Layer 2 3.2285 0.8604
STXBP1 Layer 4 3.7070 0.8600
RAB6B Layer 5 3.5215 0.8597
ARPP19 Layer 5 3.0645 0.8595
FXYD6 Layer 5 3.6836 0.8594
SLC17A7 Layer 5 3.5176 0.8589
BEX3 Layer 2 3.1113 0.8588
SNCB Layer 4 3.3359 0.8586
DSTN Layer 4 3.2148 0.8585
RTN4 Layer 2 3.0254 0.8574
ATP5IF1 Layer 2 3.1768 0.8573
APP Layer 5 3.1738 0.8573
NGRN Layer 4 3.2852 0.8572
ENC1 Layer 2 3.6133 0.8572
HSPA8 Layer 2 3.1465 0.8571
GAP43 Layer 3 3.3359 0.8570
YWHAZ Layer 5 3.2578 0.8565
PJA2 Layer 4 3.1875 0.8563
TSPAN7 Layer 2 3.4531 0.8563

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1762
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1762_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1762/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1762/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1762/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1762/report/PD/BN1762_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1762/report/PD/BN1762_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:14:15
  • Number of Processes: 10
  • Spending Time: 0h 4m